The increasing recognition of the importance of epigenetic regulation of gene expression for numerous areas of biology and medicine has led to a growing interest in this field. Despite many advances, our understanding of the molecular aspects involved in epigenetic events is still lacking and there is a growing demand for new approaches and new molecular tools to enable future advances in this field. The majority of current small molecule modulators of epigenetic regulators work by binding to the catalytic site of enzymes that modify chromatin. Because the catalytic site is often shared by multiple enzymes with distinct cellular roles, a major challenge in this area of research has been the lack of small molecules that can target a specific enzyme, which would greatly facilitate the study of the basic mechanism of epigenetic regulation and may lead to more specific and effective therapeutics. The long term objective of the research proposed in the present application is to explore a different mode of intervention of epigenetic regulators, namely by targeting protein-protein interaction in their regulatory complexes. Specifically, small molecule inhibitors will be developed for a subclass of histone deacetylases (class IIa HDACs) that are highly expressed in T cells, neurons, and muscle and are potential targets of HDAC inhibitors that showed beneficial effects in inflammation, neurodegenerative disorders, and cardiac hypertrophy The overall strategy of this proposal is to search for small molecules that block the binding of class IIa HDACs to their functional transcription factor partner, using the MEF2/HDAC interaction as a way to establish a proof of principle. Towards this goal the two principal investigators will rely on their extensive and complementary experience in structural biology and synthetic/medicinal chemistry to identify and utilize relevant molecular aspects of this problem, including: the vast amount of functional data on existing HDAC inhibitors, the availability of detailed biochemical and structural information on MEF2/HDAC interaction, and the utilization of novel chemistry-based methodologies. The basic approach is to combine structure-based modeling, targeted screen, and structure-function validation to search for such subclass specific HDAC inhibitors. Using this approach, preliminary studies have already identified several promising small molecule inhibitors of this type, that will be investigated in detail. The proposed research will further characterize the functions and properties of these molecules and establish the basis for developing new molecular probes to study HDAC function, including imaging agents and new leads for potential therapeutics for a number of major diseases. Overall, the proposed studies will serve as an example to address the feasibility of blocking protein- protein interaction in regulatory complexes as an approach to developing chemical modulators of epigenetic regulators. The new small molecule modulators of HDAC function that will be developed, are expected to be subtype specific and should help make multiple advances in the increasingly important and still emerging field of epigenetics, as well as its many applications in several disease areas. These studies will also provide new tools to study key target genes that could serve as biomarkers for diseases in the neuronal, immune and cardiovascular systems. Mechanism-based small molecule epigenetic modulators: Targeting specific HDACs PUBLIC HEALTH RELEVANCE: This application addresses broad Challenge Area (06) Enabling Technologies and it most directly relates to several Specific Challenge Topics involving Epigenetics, including the following: 06-DA-103 and 06-OD-105 "Identification of chemical modulators of epigenetic regulators";06-OD-108 "In vivo Epigenetic imaging reagents";08-AG-102 "Epigenetic changes - Identification of epigenetic changes that are specifically associated with age-related neurodegenerative diseases";03-DA-102* "Novel molecular targets from unexpected sources";03-AG-102 "Novel biomarkers for Alzheimer's disease";03-AG-103 "Biomarkers for neurodegenerative diseases";06-AG-105 "Tools facilitating chemistry and biology collaborations";03-HL-101* "Identify and validate clinically relevant, quantifiable biomarkers of diagnostic and therapeutic responses for blood, vascular, cardiac, and respiratory tract dysfunction";06-HL-107 "Develop new technologies to advance heart, lung, and blood research." The proposed research uses a novel mechanism-based approach and has the potential to discover drugs and biomarkers for multiple diseases in the neuronal, immune and cardiovascular systems.